This clinical investigation examined the effect of a single subgingival irrigation of chlorhexidine 0.2% or sanguinarine on gingivitis affecting orthodontically banded first molars in adolescent patients. Eighteen patients with gingivitis participated in the study. Probing depth, papilla bleeding index and plaque index were recorded at four sites for three molars at baseline, 2 weeks and 4 weeks by one investigator. A second investigator irrigated a single application of 3 ml of either chlorhexidine, sanguinarine or saline. The gingival bleeding as determined by papilla bleeding index was almost eliminated in the 4 week period. A reduction of the plaque index and probing depth was observed in all three groups. A significant difference related to probing depth between the effect of saline and chlorhexidine (p<0.01) was noted.